Structure of PDB 1zdq Chain B

Receptor sequence

>1zdqB (length=336) Species: 511 (Alcaligenes faecalis)

ATAAEIAALPRQKVELVDPPFVHAHSQVAEGGPKVVEFTMVIEEKKIVID
DAGTEVHAMAFNGTVPGPLMVVHQDDYLELTLINPETNTLMHNIDFHAAT
GALGGGGLTEINPGEKTILRFKATKPGVFVYHCAPPGMVPWHVVSGGNGA
IMVLPREGLHDGKGKALTYDKIYYVGEQDFYVPRDENGKYKKYEAPGDAY
EDTVKVMRTLTPTHVVFNGAVGALTGDKAMTAAVGEKVLIVHSQANRDTR
PHLIGGHGDYVWATGKFNTPPDVDQETWFIPGGAAGAAFYTFQQPGIYAY
VNHNLIEAFELGAAAHFKVTGEWNDDLMTSVLAPSG

3D structure

• PDB: 1zdq A rearranging ligand enables allosteric control of catalytic activity in copper-containing nitrite reductase.
• Chain: B
• Resolution: 1.8 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): H95 D98 H100 H135 C136 H145 G150 H255 E279 T280 H306
• Catalytic site (residue number reindexed from 1): H92 D95 H97 H132 C133 H142 G147 H252 E276 T277 H303
• Enzyme Commision number: 1.7.2.1: nitrite reductase (NO-forming).

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	CU	B	M62 H95 C136 H145	M59 H92 C133 H142
BS02	CU	B	H100 H135	H97 H132
BS03	MSM	B	W144 H145	W141 H142	MOAD: Kd=21.4mM

Gene Ontology

Molecular Function

• GO:0005507 copper ion binding
• GO:0016491 oxidoreductase activity
• GO:0046872 metal ion binding
• GO:0050421 nitrite reductase (NO-forming) activity

Biological Process

• GO:0019333 denitrification pathway
• GO:0042128 nitrate assimilation

Cellular Component

• GO:0042597 periplasmic space

External links

• PDB: RCSB:1zdq, PDBe:1zdq, PDBj:1zdq
• PDBsum: 1zdq
• PubMed: 16574144
• UniProt: P38501|NIR_ALCFA Copper-containing nitrite reductase (Gene Name=nirK)